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# Copyright 2009-2011 by Eric Talevich. All rights reserved.
# Revisions copyright 2009-2013 by Peter Cock. All rights reserved.
# Revisions copyright 2013 Lenna X. Peterson. All rights reserved.
# Revisions copyright 2020 Joao Rodrigues. All rights reserved.
#
# Converted by Eric Talevich from an older unit test copyright 2002
# by Thomas Hamelryck.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Unit tests for the Bio.PDB.MMCIFIO module."""
import os
import tempfile
import unittest
import warnings
from Bio import BiopythonWarning
from Bio.PDB import MMCIFParser, MMCIFIO, PDBParser, Select
from Bio.PDB import Atom, Residue
from Bio.PDB.MMCIF2Dict import MMCIF2Dict
from Bio.PDB.PDBExceptions import PDBConstructionException, PDBConstructionWarning
class WriteTest(unittest.TestCase):
@classmethod
def setUpClass(self):
self.io = MMCIFIO()
self.mmcif_parser = MMCIFParser()
self.pdb_parser = PDBParser()
with warnings.catch_warnings():
warnings.simplefilter("ignore", PDBConstructionWarning)
self.structure = self.pdb_parser.get_structure("example", "PDB/1A8O.pdb")
self.mmcif_file = "PDB/1A8O.cif"
self.mmcif_multimodel_pdb_file = "PDB/1SSU_mod.pdb"
self.mmcif_multimodel_mmcif_file = "PDB/1SSU_mod.cif"
def test_mmcifio_write_structure(self):
"""Write a full structure using MMCIFIO."""
struct1 = self.structure
# Write full model to temp file
self.io.set_structure(struct1)
filenumber, filename = tempfile.mkstemp()
os.close(filenumber)
try:
self.io.save(filename)
struct2 = self.mmcif_parser.get_structure("1a8o", filename)
nresidues = len(list(struct2.get_residues()))
self.assertEqual(len(struct2), 1)
self.assertEqual(nresidues, 158)
finally:
os.remove(filename)
def test_mmcifio_write_residue(self):
"""Write a single residue using MMCIFIO."""
struct1 = self.structure
residue1 = list(struct1.get_residues())[0]
# Write full model to temp file
self.io.set_structure(residue1)
filenumber, filename = tempfile.mkstemp()
os.close(filenumber)
try:
self.io.save(filename)
struct2 = self.mmcif_parser.get_structure("1a8o", filename)
nresidues = len(list(struct2.get_residues()))
self.assertEqual(nresidues, 1)
finally:
os.remove(filename)
def test_mmcifio_write_residue_w_chain(self):
"""Write a single residue (chain id == X) using MMCIFIO."""
struct1 = self.structure.copy() # make copy so we can change it
residue1 = list(struct1.get_residues())[0]
# Modify parent id
parent = residue1.parent
parent.id = "X"
# Write full model to temp file
self.io.set_structure(residue1)
filenumber, filename = tempfile.mkstemp()
os.close(filenumber)
try:
self.io.save(filename)
struct2 = self.mmcif_parser.get_structure("1a8o", filename)
nresidues = len(list(struct2.get_residues()))
self.assertEqual(nresidues, 1)
# Assert chain remained the same
chain_id = [c.id for c in struct2.get_chains()][0]
self.assertEqual(chain_id, "X")
finally:
os.remove(filename)
def test_mmcifio_write_residue_wout_chain(self):
"""Write a single orphan residue using MMCIFIO."""
struct1 = self.structure
residue1 = list(struct1.get_residues())[0]
residue1.parent = None # detach residue
# Write full model to temp file
self.io.set_structure(residue1)
filenumber, filename = tempfile.mkstemp()
os.close(filenumber)
try:
self.io.save(filename)
struct2 = self.mmcif_parser.get_structure("1a8o", filename)
nresidues = len(list(struct2.get_residues()))
self.assertEqual(nresidues, 1)
# Assert chain is default: "A"
chain_id = [c.id for c in struct2.get_chains()][0]
self.assertEqual(chain_id, "A")
finally:
os.remove(filename)
def test_mmcifio_write_custom_residue(self):
"""Write a chainless residue using PDBIO."""
res = Residue.Residue((" ", 1, " "), "DUM", "")
atm = Atom.Atom("CA", [0.1, 0.1, 0.1], 1.0, 1.0, " ", "CA", 1, "C")
res.add(atm)
# Ensure that set_structure doesn't alter parent
parent = res.parent
# Write full model to temp file
self.io.set_structure(res)
self.assertIs(parent, res.parent)
filenumber, filename = tempfile.mkstemp()
os.close(filenumber)
try:
self.io.save(filename)
struct2 = self.mmcif_parser.get_structure("res", filename)
latoms = list(struct2.get_atoms())
self.assertEqual(len(latoms), 1)
self.assertEqual(latoms[0].name, "CA")
self.assertEqual(latoms[0].parent.resname, "DUM")
self.assertEqual(latoms[0].parent.parent.id, "A")
finally:
os.remove(filename)
def test_mmcifio_select(self):
"""Write a selection of the structure using a Select subclass."""
# Selection class to filter all alpha carbons
class CAonly(Select):
"""Accepts only CA residues."""
def accept_atom(self, atom):
if atom.name == "CA" and atom.element == "C":
return 1
struct1 = self.structure
# Write to temp file
self.io.set_structure(struct1)
filenumber, filename = tempfile.mkstemp()
os.close(filenumber)
try:
self.io.save(filename, CAonly())
struct2 = self.mmcif_parser.get_structure("1a8o", filename)
nresidues = len(list(struct2.get_residues()))
self.assertEqual(nresidues, 70)
finally:
os.remove(filename)
def test_mmcifio_write_dict(self):
"""Write an mmCIF dictionary out, read it in and compare them."""
d1 = MMCIF2Dict(self.mmcif_file)
# Write to temp file
self.io.set_dict(d1)
filenumber, filename = tempfile.mkstemp()
os.close(filenumber)
try:
self.io.save(filename)
d2 = MMCIF2Dict(filename)
k1 = sorted(d1.keys())
k2 = sorted(d2.keys())
self.assertEqual(k1, k2)
for key in k1:
self.assertEqual(d1[key], d2[key])
finally:
os.remove(filename)
def test_mmcifio_multimodel(self):
"""Write a multi-model, multi-chain mmCIF file."""
pdb_struct = self.pdb_parser.get_structure(
"1SSU_mod_pdb", self.mmcif_multimodel_pdb_file
)
mmcif_struct = self.mmcif_parser.get_structure(
"1SSU_mod_mmcif", self.mmcif_multimodel_mmcif_file
)
io = MMCIFIO()
for struct in [pdb_struct, mmcif_struct]:
self.io.set_structure(struct)
filenumber, filename = tempfile.mkstemp()
os.close(filenumber)
try:
self.io.save(filename)
struct_in = self.mmcif_parser.get_structure("1SSU_mod_in", filename)
self.assertEqual(len(struct_in), 2)
self.assertEqual(len(struct_in[1]), 2)
self.assertEqual(
round(float(struct_in[1]["B"][1]["N"].get_coord()[0]), 3), 6.259
)
finally:
os.remove(filename)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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